Publications

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

Wang H, Xu X, Nguyen CM, Liu Y, Gao Y, Lin X, Daley TP, Kipniss NH, La Russa M, Qi LS.

Cell 175, 1–13. 2018 Oct 11.

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

Liu Y*, Yu C*, Daley TP*, Wang F, Cao WS, Bhate S, Lin X, Still C, Liu H, Zhao D, Wang H, Xie XS, Ding S, Wong WH, Wernig M, Qi LS.

Cell Stem Cell 23: 1-4. 2018 Oct 11. (*Equal Contribution)

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens

Daley TP, Lin Z, Lin X, Liu Y, Wong WH, Qi LS. 

Genome Biol.19:159. 2018 Oct 8

A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology

Xu X, Qi LS. 

J Mol. Biol. pii: S0022-2836(18)30666-1 2018 Jun 28. (Review)

CRISPR-Based Chromatin Remodeling of the Endogenous Oct4 or Sox2 Locus Enables Reprogramming to Pluripotency

Liu P, Chen M, Liu Y, Qi LS, Ding S. 

Cell Stem Cell 2018 Jan 18

Engineering Cell Sensing and Responses Using a GPCR-Coupled CRISPR-Cas System

Kipniss NK*, Dingal PCDP*, Abbott TR, Gao Y, Wang H, Dominguez AA, Labanieh L, Qi LS. 

Nat. Comm. 8(1):2212 2017 Dec 20 (*Equal contribution)

A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription

Zhou XX, Zou X, Chung HK, Gao Y, Liu Y, Qi LS, Lin MZ

ACS Chem. Biol. 2017 Sep 29

Genetic and epigenetic control of gene expression by CRISPR-Cas systems

Lo A, Qi LS

F1000 Research 6:747. 2017 May 25. (Review)

Genetic interaction mapping in mammalian cells using CRISPR interference

Du D#, Roguez A#, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS*, Krogan NJ*

Nature Methods. 14(6):577-580. 2017 May 8.

(#Equal Contribution; *Co-corresponding)

Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH

Takei Y, Shah S, Harvey S, Qi LS, Cai L. 

Biophys J. 112: 1173-1176. 2017 Apr 17.

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions

Shen JP, Zhao D, Sasik R, Luebeck K, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguez A, Lewis NE, Chang AN, Kreisberg JF, Krogan NJ, Qi LS, Ideker T, Mali P

Nat Methods. 14(6):573-576. 2017 Mar 20.    

Complex Transcriptional Modulation with Orthogonal and Inducible dCas9 Regulators

Gao Y*, Xiong X*, Wong S, Charles EJ, Lim WA, Qi LS. 

Nature Methods 13:1043-1049. 2016 Oct 24. (*Equal Contribution)

Applications of CRISPR Genome Engineering in Cell Biology

Wang F, Qi LS  

Trends Cell Biol. 26:875-888. 2016 Nov

A Comprehensive, CRISPR-Based Approach to Functional Analysis of Essential Genes in Bacteria

Peters JM, Colavin A, Shi H, Czarny ML, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS*, Huang KC*, Gross CA*. 

Cell 165: 1493-1506. 2016 June 2. (*Co-corresponding)  

CRISPR/Cas9 for Human Genome Engineering and Disease Research

Xiong X, Chen M, Lim WA, Zhao D, Qi LS.

Annu. Rev. Genomics Hum. Genet. 2016 May 23 (Review)

CRISPR-Cas9 in Genome Editing and Beyond

Wang H, La Russa M, Qi LS. 

Annu. Rev. Biochem. 85:22.1–22.38  2016 Apr 15. (Review)

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs

Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Chan AH, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR.    

Cell Stem Cell. 18: 541–543. 2016 Apr 7. 

YAP Induces Human Naïve Pluripotency

Qin H, Hejna M, Liu Y, Percharde M, Wossidlo M, Blouin L, Durruthy-Durruthy J, Wong P, Qi Z, Yu J, Qi LS, Sebastiano V, Song JS, Ramalho-Santos M.

Cell Reports. 14: 2301–2312. 2016 Mar 15

Beyond Editing: Repurposing CRISPR-Cas9 for Precision Genome Regulation and Interrogation 

Dominguze AA, Lim WA*, Qi LS*.

Nat. Rev. Mol. Cell. Biol. 17, 5–15; 2016 Jan (Review) (*Co-corresponding)  

CRISPR Technology for Genome Activation and Repression in Mammalian Cells

Du D, Qi LS.

Cold Spring Harb. Protoc. 2016: pdb.top086835. &  2016: pdb.prot090175. 2016 Jan 4 (Protocol)

The New State of the Art: Cas9 for Gene Activation and Repression

La Russa MF, Qi LS. 

Mol. Cell Biol. 35(22): 3800-3809. 2015 Nov 15. (Review)

Bacterial CRISPR: Accomplishments and Prospects

Peters JM, Silvis MR, Zhao D, Hawkins JS, Gross CA*, Qi LS*. 

Curr. Opin. Microbiol. 27: 121-126; 2015 October 30. (Review) (*Co-corresponding)  

Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise

Sokolik C, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi LS, Sivak DA, Thomson M.

Cell Systems. 1(2): 117-129; 2015 August 26.

CRISPR-ERA: A Comprehensive Designer Tool for CRISPR-Mediated Gene Editing, Repression and Activation 

Liu H, Wei Z, Dominguez A, Li Y, Wang X*, Qi LS*.

Bioinformatics. 31(22):3676-8; 2015 Nov 15. (*Co-corresponding)  

Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi) 

Hawkins JS, Wong S, Peters JM, Almeida R, Qi LS.

Methods Mol. Biol. 1311: 349-362; 2015 June.

Small Molecules Enhance CRISPR Genome Editing in Pluripotent Stem Cells

Yu C, Liu Y, Ma T, Xu S, Liu K, Zhang Y, La Russa M, Xie M, Ding S*, Qi LS*.

Cell Stem Cell. 16(2):142-147; 2015 Feb 5. (*Co-corresponding)  

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

Zalatan JG, Lee ME, Gilbert LA, Almeida R, Tsai JC, Whitehead EH, Weissman JS, Dueber JE, Qi LS*, Lim WA*.

Cell 160:339-350; 2015 Jan 15. (*Co-corresponding)  

The article is selected as cover art of Cell for that issue. On the cover: CRISPR RNA scaffolds (scRNAs) navigate the genome to direct the CRISPR-Cas complex to specific target genes. Zalatan et al. (pp. 339–350) demonstrate that each scRNA encodes a DNA target and the function to execute at the target, so that sets of scRNAs can be used to generate a synthetic, multigene transcriptional program in which some genes are activated and others are repressed. Artwork by Jennifer Sunami.

Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation

Ji W, Lee D, Wong E, Dadlani P, Dinh D, Huang V, Kearns K, Teng S, Chen S, Haliburton J, Heimberg G, Heineike B, Ramasubramanian A, Stevens T, Helmke KJ, Zepeda V, Qi LS, Lim WA.

ACS Synth Biol. 3(12):929-31; 2014 Dec 19.

A Versatile Protein Tagging System for Signal Amplification in Single Molecule Imaging and Gene Regulation

Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD.

Cell. 159(3):635-646; 2014 Oct 23.

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS.

Cell. 159(3):647-661; 2014 Oct 23.

A Versatile Platform for Microbial Engineering using Synthetic Noncoding RNAs

Qi LS*, Arkin AP*. (*Corresponding authors)

Nat. Rev. Microbiol. 12(5):341-354; 2014 April 14. (Review) 

Dynamic Imaging of Genomic Loci in Living Human Cells by An Optimized CRISPR/Cas System

Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS*, Huang B*. 

Cell 155(7):1479-1491; 2013 Dec 19. (*Co-corresponding)

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS.

Cell 154(2):442-451; 2013 Jul 18.

CRISPR Interference (CRISPRi) for Sequence-Specific Control of Gene Expression

Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS*.

Nat. Protoc. 8(11): 2108-2196; 2013 Oct 17.

Repurposing CRISPR as An RNA-guided Platform for Sequence-Specific Control of Gene Expression

Qi LS*, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. 

Cell 152(5):1173-1183; 2013 Feb 28. (*Corresponding and first author)

RNA Processing Enables Predictable Programming of Gene Expression

Qi LS, Haurwitz RE, Shao WJ, Doudna JA, Arkin AP.

Nat. Biotechnol. 30(10):1002-1006; 2012 Sept 16.

An Adaptor from Translational to Transcriptional Control Enables Predictable Assembly of Complex Regulation

Liu CC*, Qi LS*, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VM, Arkin AP. 

Nat. Methods. 9(11):1088-1094; 2012 Sept 30. (* Equal Contribution)

Engineering Naturally Occurring Trans-Acting Non-Coding RNAs to Sense Molecular Signals

Qi LS, Lucks JB, Liu CC, Mutalik VK, Arkin AP.

Nucleic Acids Res. 40(12):5775-5786; 2012 March 1.

Rationally Designed Families of Orthogonal RNA Regulators of Translation

Mutalik VK*, Qi LS*, Guimaraes JC, Lucks JB, Arkin AP. 

Nat. Chem. Biol. 8(5):447-454; 2012 March 25. (* Equal contribution)

Versatile RNA-Sensing Transcriptional Regulators for Engineering Genetic Networks

Lucks JB*, Qi LS*, Mutalik VK, Wang D, Arkin AP. 

Proc. Natl Acad. Sci. USA 108(21):8617-8822; 2011 May 24. (*Equal contribution)

Regulation of Transcription by Unnatural Amino Acids

Liu CC, Qi LS, Yanofsky C, Arkin AP.

Nat. Biotechnol. 29(2):164-168; 2011 Jan 16.

Toward Scalable Parts Families for Predictable Design of Biological Circuits

Lucks JB, Qi LS, Whitaker WR, Arkin AP.

Curr. Opin. Microbiol. 11(6):567-573; 2008 Dec. (Review)